Coarse-graining involving virtual sites: Centers of symmetry coarse-graining

Ultra-Coarse-Grained Models Allow for an Accurate and Transferable Treatment of Interfacial Systems

(2018) Jaehyeok Jin et al.   Journal of Chemical Theory and Computation

Extending the range and physical accuracy of coarse-grained models: Order parameter dependent interactions

(2017) Jacob W. Wagner et al.   JOURNAL OF CHEMICAL PHYSICS

Highly Coarse-Grained Representations of Transmembrane Proteins

(2017) Jesper J. Madsen et al.   Journal of Chemical Theory and Computation

The Theory of Ultra-Coarse-Graining. 3. Coarse-Grained Sites with Rapid Local Equilibrium of Internal States

(2017) James F. Dama et al.   Journal of Chemical Theory and Computation

Van der Waals Perspective on Coarse-Graining: Progress toward Solving Representability and Transferability Problems

(2016) Nicholas J. H. Dunn et al.   ACCOUNTS OF CHEMICAL RESEARCH

Coarse-Grained Protein Models and Their Applications

(2016) Sebastian Kmiecik et al.   CHEMICAL REVIEWS

A coarse grained protein model with internal degrees of freedom. Application to α-synuclein aggregation

(2016) Ioana M. Ilie et al.   JOURNAL OF CHEMICAL PHYSICS

Multiscale Coarse-Graining of Polarizable Models through Force-Matched Dipole Fluctuations

(2016) Patrick G. Lafond et al.   Journal of Chemical Theory and Computation

TMFF—A Two-Bead Multipole Force Field for Coarse-Grained Molecular Dynamics Simulation of Protein

(2016) Min Li et al.   Journal of Chemical Theory and Computation

Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly

(2016) John M. A. Grime et al.   Nature Communications

The impact of resolution upon entropy and information in coarse-grained models

(2015) Thomas T. Foley et al.   JOURNAL OF CHEMICAL PHYSICS

The multiscale coarse-graining method. XI. Accurate interactions based on the centers of charge of coarse-grained sites

(2015) Zhen Cao et al.   JOURNAL OF CHEMICAL PHYSICS

Role of Backbone Dipole Interactions in the Formation of Secondary and Supersecondary Structures of Proteins

(2014) Sai J. Ganesan et al.   Journal of Chemical Theory and Computation

Solvent-Free, Highly Coarse-Grained Models for Charged Lipid Systems

(2014) Anand Srivastava et al.   Journal of Chemical Theory and Computation

Coarse-Graining Methods for Computational Biology

(2013) Marissa G. Saunders et al.   Annual Review of Biophysics

Perspective on the Martini model

(2013) Siewert J. Marrink et al.   CHEMICAL SOCIETY REVIEWS

Minimizing memory as an objective for coarse-graining

(2013) Nicholas Guttenberg et al.   JOURNAL OF CHEMICAL PHYSICS

Perspective: Coarse-grained models for biomolecular systems

(2013) W. G. Noid   JOURNAL OF CHEMICAL PHYSICS

Early Stages of the HIV-1 Capsid Protein Lattice Formation

(2012) John M.A. Grime et al.   BIOPHYSICAL JOURNAL

The multiscale coarse-graining method. X. Improved algorithms for constructing coarse-grained potentials for molecular systems

(2012) Avisek Das et al.   JOURNAL OF CHEMICAL PHYSICS

Hybrid Approach for Highly Coarse-Grained Lipid Bilayer Models

(2012) Anand Srivastava et al.   Journal of Chemical Theory and Computation

Optimal Number of Coarse-Grained Sites in Different Components of Large Biomolecular Complexes

(2012) Anton V. Sinitskiy et al.   JOURNAL OF PHYSICAL CHEMISTRY B

SAFT-γforce field for the simulation of molecular fluids: 3. Coarse-grained models of benzene and hetero-group models ofn-decylbenzene

(2012) Thomas Lafitte et al.   MOLECULAR PHYSICS

Using sketch-map coordinates to analyze and bias molecular dynamics simulations

(2012) G. A. Tribello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nonlinear dimensionality reduction in molecular simulation: The diffusion map approach

(2011) Andrew L. Ferguson et al.   CHEMICAL PHYSICS LETTERS

Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent

(2011) Johnny Wu et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse-graining errors and numerical optimization using a relative entropy framework

(2011) Aviel Chaimovich et al.   JOURNAL OF CHEMICAL PHYSICS

Simplifying the representation of complex free-energy landscapes using sketch-map

(2011) Michele Ceriotti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials

(2010) Luca Larini et al.   JOURNAL OF CHEMICAL PHYSICS

Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining

(2010) Lanyuan Lu et al.   Journal of Chemical Theory and Computation

Relative entropy as a universal metric for multiscale errors

(2010) Aviel Chaimovich et al.   PHYSICAL REVIEW E

Systematic determination of order parameters for chain dynamics using diffusion maps

(2010) A. L. Ferguson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Defining Coarse-Grained Representations of Large Biomolecules and Biomolecular Complexes from Elastic Network Models

(2009) Zhiyong Zhang et al.   BIOPHYSICAL JOURNAL

Assessment of standard force field models against high-qualityab initiopotential curves for prototypes of π-π, CH/π, and SH/π interactions

(2009) C. David Sherrill et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

PACKMOL: A package for building initial configurations for molecular dynamics simulations

(2009) L. Martínez et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A Generalized-Yvon−Born−Green Theory for Determining Coarse-Grained Interaction Potentials

(2009) J. W. Mullinax et al.   Journal of Physical Chemistry C

Generalized Yvon-Born-Green Theory for Molecular Systems

(2009) J. W. Mullinax et al.   PHYSICAL REVIEW LETTERS

Four-Scale Description of Membrane Sculpting by BAR Domains

(2008) Anton Arkhipov et al.   BIOPHYSICAL JOURNAL

A Systematic Methodology for Defining Coarse-Grained Sites in Large Biomolecules

(2008) Zhiyong Zhang et al.   BIOPHYSICAL JOURNAL

Computational techniques for efficient conformational sampling of proteins

(2008) Adam Liwo et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

(2008) W. G. Noid et al.   JOURNAL OF CHEMICAL PHYSICS

A novel algorithm for creating coarse-grained, density dependent implicit solvent models

(2008) Erik C. Allen et al.   JOURNAL OF CHEMICAL PHYSICS

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

(2008) W. G. Noid et al.   JOURNAL OF CHEMICAL PHYSICS

The relative entropy is fundamental to multiscale and inverse thermodynamic problems

(2008) M. Scott Shell   JOURNAL OF CHEMICAL PHYSICS

Benzene Dimer: High-Level Wave Function and Density Functional Theory Calculations

(2008) M. Pitoňák et al.   Journal of Chemical Theory and Computation

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

The Impact of Conformational Fluctuations on Self-Assembly: Cooperative Aggregation of Archaeal Chaperonin Proteins

(2008) Stephen Whitelam et al.   NANO LETTERS

A transferable coarse-grained model for hydrogen-bonding liquids

(2008) Pavel A. Golubkov et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS